It is started with a few "founder" stock, who are then bred and the F1 offspring with the so called "desirable "traits are bred to each other . There is a lot of close incest, parent to child and brother to sister to "fix" the desired traits ( desirable to man that is) like the ridge on the ridgeback dog or the flat face or the dwarf legs and after several generations of this the new breed becomes clonelike or uniform and established as all the members are homozygotes ( carrying like genes). It becomes a breed when all the offspring are alike , ie dalmations or border collies. But incest is still used frequently to "keep it in the family" or to maintain like features. All matings are planned and the unnatural changes derived from wild stock come around from breeding from mutations.
First they take an skin cell from an animal or living thing and then they take the sex cell and they put the sex cells nucleus into the skin cell and get rid of the skin cell nucleus